data_5CJW # _model_server_result.job_id KMM-46_e3hi7Fy0dZqAgOw _model_server_result.datetime_utc '2024-11-15 02:03:33' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5cjw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1102}' # _entry.id 5CJW # _exptl.entry_id 5CJW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 251.242 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXYADENOSINE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 5CJW _cell.length_a 317.52 _cell.length_b 317.52 _cell.length_c 343.04 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CJW _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 59 A HIS 39 1_555 C CO B12 . A B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc2 A OG SER 243 A SER 223 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc5 A OD2 ASP 282 A ASP 262 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc6 A OE2 GLU 330 A GLU 310 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc7 A OE2 GLU 330 A GLU 310 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc8 C CO B12 . A B12 1101 1_555 D C5' 5AD . A 5AD 1102 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.145 ? metalc ? metalc9 F O2B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc10 F O3B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc11 B NE2 HIS 59 B HIS 39 1_555 I CO B12 . B B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc12 B OG SER 243 B SER 223 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc13 B O ILE 268 B ILE 248 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc14 B OD1 ASP 269 B ASP 249 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc15 B OD1 ASP 282 B ASP 262 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc16 B OD2 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc17 B OE2 GLU 330 B GLU 310 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc18 B OE2 GLU 330 B GLU 310 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc19 B O THR 331 B THR 311 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? metalc ? metalc20 K O2B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc21 K O3B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? # _chem_comp.formula 'C10 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 5AD _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXYADENOSINE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 5AD doub 101 n y N1 C6 5AD sing 102 n y C2 N3 5AD sing 103 n y C2 H2 5AD sing 104 n n N3 C4 5AD doub 105 n y C4 N9 5AD sing 106 n y C4 C5 5AD sing 107 n y N9 C8 5AD sing 108 n y N9 C1' 5AD sing 109 n n C8 N7 5AD doub 110 n y C8 H8 5AD sing 111 n n N7 C5 5AD sing 112 n y C5 C6 5AD doub 113 n y C6 N6 5AD sing 114 n n N6 HN61 5AD sing 115 n n N6 HN62 5AD sing 116 n n C1' C2' 5AD sing 117 n n C1' O4' 5AD sing 118 n n C1' H1' 5AD sing 119 n n C2' C3' 5AD sing 120 n n C2' O2' 5AD sing 121 n n C2' H2' 5AD sing 122 n n C3' C4' 5AD sing 123 n n C3' O3' 5AD sing 124 n n C3' H3' 5AD sing 125 n n C4' C5' 5AD sing 126 n n C4' O4' 5AD sing 127 n n C4' H4' 5AD sing 128 n n C5' "H5'1" 5AD sing 129 n n C5' "H5'2" 5AD sing 130 n n C5' "H5'3" 5AD sing 131 n n O2' HO2' 5AD sing 132 n n O3' HO3' 5AD sing 133 n n # _atom_sites.entry_id 5CJW _atom_sites.fract_transf_matrix[1][1] 0.003149 _atom_sites.fract_transf_matrix[1][2] 0.001818 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003637 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.002915 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 B12 A 1 1101 1198 B12 B12 . D 3 5AD A 1 1102 1199 5AD 5AD . E 4 52O A 1 1103 1211 52O XXX . F 5 GDP A 1 1104 1200 GDP GDP . G 6 MG A 1 1105 1 MG MG . H 6 MG A 1 1106 3 MG MG . I 2 B12 B 1 1101 1198 B12 B12 . J 4 52O B 1 1102 1211 52O XXX . K 5 GDP B 1 1103 1201 GDP GDP . L 6 MG B 1 1104 2 MG MG . M 6 MG B 1 1105 4 MG MG . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 5AD . A . D 3 -217.652 -103.038 -9.955 0.5 177.07 ? N1 5AD 1102 A 1 HETATM 2 N N1 5AD . B . D 3 -217.934 -102.544 -10.389 0.5 176.26 ? N1 5AD 1102 A 1 HETATM 3 C C2 5AD . A . D 3 -218.048 -102.157 -10.878 0.5 174.92 ? C2 5AD 1102 A 1 HETATM 4 C C2 5AD . B . D 3 -218.172 -101.468 -11.145 0.5 174.56 ? C2 5AD 1102 A 1 HETATM 5 N N3 5AD . A . D 3 -217.753 -100.858 -10.98 0.5 176.26 ? N3 5AD 1102 A 1 HETATM 6 N N3 5AD . B . D 3 -217.689 -100.229 -11.016 0.5 175.61 ? N3 5AD 1102 A 1 HETATM 7 C C4 5AD . A . D 3 -216.946 -100.469 -9.984 0.5 173.17 ? C4 5AD 1102 A 1 HETATM 8 C C4 5AD . B . D 3 -216.868 -100.141 -9.962 0.5 173.78 ? C4 5AD 1102 A 1 HETATM 9 N N9 5AD . A . D 3 -216.428 -99.215 -9.77 0.5 176.62 ? N9 5AD 1102 A 1 HETATM 10 N N9 5AD . B . D 3 -216.187 -99.031 -9.524 0.5 175.69 ? N9 5AD 1102 A 1 HETATM 11 C C8 5AD . A . D 3 -215.67 -99.316 -8.633 0.5 176.38 ? C8 5AD 1102 A 1 HETATM 12 C C8 5AD . B . D 3 -215.487 -99.438 -8.418 0.5 176.84 ? C8 5AD 1102 A 1 HETATM 13 N N7 5AD . A . D 3 -215.652 -100.518 -8.108 0.5 175.67 ? N7 5AD 1102 A 1 HETATM 14 N N7 5AD . B . D 3 -215.656 -100.702 -8.115 0.5 175.72 ? N7 5AD 1102 A 1 HETATM 15 C C5 5AD . A . D 3 -216.458 -101.261 -8.958 0.5 178.85 ? C5 5AD 1102 A 1 HETATM 16 C C5 5AD . B . D 3 -216.529 -101.161 -9.089 0.5 179.09 ? C5 5AD 1102 A 1 HETATM 17 C C6 5AD . A . D 3 -216.839 -102.616 -8.96 0.5 174.63 ? C6 5AD 1102 A 1 HETATM 18 C C6 5AD . B . D 3 -217.101 -102.425 -9.332 0.5 174.32 ? C6 5AD 1102 A 1 HETATM 19 N N6 5AD . A . D 3 -216.439 -103.502 -8.044 0.5 176.87 ? N6 5AD 1102 A 1 HETATM 20 N N6 5AD . B . D 3 -216.861 -103.504 -8.583 0.5 177.38 ? N6 5AD 1102 A 1 HETATM 21 C C1' 5AD . A . D 3 -216.613 -98.032 -10.603 0.5 173.92 ? C1' 5AD 1102 A 1 HETATM 22 C C1' 5AD . B . D 3 -216.185 -97.699 -10.119 0.5 174.01 ? C1' 5AD 1102 A 1 HETATM 23 C C2' 5AD . A . D 3 -217.749 -97.105 -10.151 0.5 173.86 ? C2' 5AD 1102 A 1 HETATM 24 C C2' 5AD . B . D 3 -217.375 -96.833 -9.711 0.5 173.52 ? C2' 5AD 1102 A 1 HETATM 25 C C3' 5AD . A . D 3 -216.991 -95.998 -9.418 0.5 172.73 ? C3' 5AD 1102 A 1 HETATM 26 C C3' 5AD . B . D 3 -216.774 -95.433 -9.824 0.5 171.89 ? C3' 5AD 1102 A 1 HETATM 27 C C4' 5AD . A . D 3 -215.69 -95.918 -10.203 0.5 172.26 ? C4' 5AD 1102 A 1 HETATM 28 C C4' 5AD . B . D 3 -215.336 -95.648 -9.353 0.5 172.08 ? C4' 5AD 1102 A 1 HETATM 29 C C5' 5AD . A . D 3 -214.505 -95.364 -9.45 0.5 171.42 ? C5' 5AD 1102 A 1 HETATM 30 C C5' 5AD . B . D 3 -215.088 -95.423 -7.881 0.5 172.68 ? C5' 5AD 1102 A 1 HETATM 31 O O4' 5AD . A . D 3 -215.413 -97.279 -10.584 0.5 173.46 ? O4' 5AD 1102 A 1 HETATM 32 O O4' 5AD . B . D 3 -215.022 -97.019 -9.682 0.5 173.02 ? O4' 5AD 1102 A 1 HETATM 33 O O2' 5AD . A . D 3 -218.458 -96.604 -11.278 0.5 173.75 ? O2' 5AD 1102 A 1 HETATM 34 O O2' 5AD . B . D 3 -218.462 -97.021 -10.609 0.5 173.72 ? O2' 5AD 1102 A 1 HETATM 35 O O3' 5AD . A . D 3 -217.662 -94.746 -9.505 0.5 172.21 ? O3' 5AD 1102 A 1 HETATM 36 O O3' 5AD . B . D 3 -216.76 -94.97 -11.169 0.5 170.87 ? O3' 5AD 1102 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #